Just a heads up, this is the WJ forum, you have a ZJ...
What did you clean your intake manifold with? Water from the tail pipe isn't a problem, it's a by-product of combustion (obviously unless it's pouring out), and there will be carbon buildup throughout your exhaust as well (same principal). Any idle fluctuations after a repair that wasn't present before said repair should be an easy fix. There are multiple vacuum lines on the intake manifold, did you check all of them? Is everything plugged in? Is the CEL on? I'm not sure what fuel line you're talking about, can you take a picture?
PSA - It would be nice if people made an attempt while typing to discuss their problems or opinions instead of one long sentence with no punctuation. Maybe I'm cynical, but that really pisses me off. Rant over.
"It's like saying I had a car I got that was painted by the previous owner. I had an accident so painting a car is unsafe." - cykaaro